Genotyping remains a rate limiting step in localizing disease genes since it is highly technical, time consuming, and expensive. The long term objective is to develop a two step fluorescence based automated system that will improve the efficiency and accuracy of genotyping. Ninety genetic markers have already been combined for use as the first step in genomic analyses (Phase I SBIR). The examination of specific chromosomal regions in a second step is accomplished using higher resolution systems. The aims of the current proposal are to develop a second stage fluorescence based system by combining 744 genetic markers into 124 sets (6 markers each). The markers for each set will be selected from a single region covering approximately 30 centimorgans (cM) of the genome. This system will be compatible with all existing automated fluorescence based marker detection hardware. Commercial application of the technology also could benefit by the aims to develop a simple novel chromogenic assay in a pipette tip to confirm when a fluorescent labeled PCR product is produced; and a pipette tip that enables the purification of multiple biotinylated PCR products maximizing signal to noise. This automated technology may be useful in linkage, paternity testing, cancer genetics, forensics, and cytogenetics.